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strelka2_AD field is improperly formatted for multi-allelic variants

Status: Open.

#46 In NCI-CGR/GEMSCAN;

· LauraEgolf opened on Jul 9, 2025

temp directory is having issues

Status: Open.

#44 In NCI-CGR/GEMSCAN;

· shukwong opened on May 1, 2024

implement Harmonize mode only

enhancementNew feature or requestNew feature or request

Status: Open.

#40 In NCI-CGR/GEMSCAN;

· shukwong opened on Mar 22, 2023

The workflow skips many steps if the bed file contains only 1 line

bugSomething isn't workingSomething isn't working

Status: Open.

#39 In NCI-CGR/GEMSCAN;

· shukwong opened on Jan 27, 2023

move Docker registry from quay.io to ghcr.io

enhancementNew feature or requestNew feature or request

Status: Open.

#36 In NCI-CGR/GEMSCAN;

· shukwong opened on Apr 6, 2022

prepend_labels for strelka calls runs longer than 2 hours

enhancementNew feature or requestNew feature or request

Status: Open.

#35 In NCI-CGR/GEMSCAN;

· shukwong opened on Jan 18, 2022

fixing the symlinks in strelka2_AddSampleName rule

bugSomething isn't workingSomething isn't working

Status: Open.

#34 In NCI-CGR/GEMSCAN;

· shukwong opened on Dec 14, 2021

GLnexus merge memory requirements calculation

enhancementNew feature or requestNew feature or request

Status: Open.

#33 In NCI-CGR/GEMSCAN;

· shukwong opened on Dec 1, 2021

handle alternate contigs and scaffolds in bed file

Status: Open.

#30 In NCI-CGR/GEMSCAN;

· shukwong opened on Oct 15, 2021

write a script to generate the samples.txt from a directory with BAM/cram files

enhancementNew feature or requestNew feature or request

Status: Open.

#29 In NCI-CGR/GEMSCAN;

· shukwong opened on Aug 3, 2021

set default path to glnexus_strelka2_config

enhancementNew feature or requestNew feature or request

Status: Open.

#28 In NCI-CGR/GEMSCAN;

· shukwong opened on Jul 15, 2021

add support for remote files on object store as input on Biowulf

enhancementNew feature or requestNew feature or request

Status: Open.

#25 In NCI-CGR/GEMSCAN;

· shukwong opened on Jul 2, 2021